BioC 3.1: CHECK report for genoset on petty

Package: genoset

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.22.0.tar.gz

StartedAt: 2015-10-08 23:17:54 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:21:27 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 213.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genoset.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/genoset.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genoset’ can be installed ... [29s/29s] WARNING
Found the following significant warnings:
  Warning: subclass "GNCList" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "GIntervalTree" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/Users/biocbuild/bbs-3.1-bioc/meat/genoset.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... WARNING
Found .Internal calls in methods for the following S4 generics:
  ‘rowMeans’ ‘rowSums’

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.

In addition to the above warning(s), found the following notes:

calcGC : <anonymous>: no visible global function definition for ‘Views’
calcGC : <anonymous>: no visible global function definition for
  ‘alphabetFrequency’
initGenoSet: no visible global function definition for ‘universe<-’
initGenoSet: no visible global function definition for
  ‘assayDataValidMembers’
[<-,GenoSet-ANY-ANY-ANY : .local: no visible global function definition
  for ‘assayDataElement<-’
colnames,GenoSet : .local: no visible global function definition for
  ‘pData’
colnames<-,GenoSet: no visible global function definition for ‘pData’
colnames<-,GenoSet: no visible global function definition for ‘pData<-’
colnames<-,GenoSet: no visible global function definition for
  ‘assayData’
colnames<-,GenoSet: no visible global function definition for
  ‘assayData<-’
dim,GenoSet: no visible global function definition for ‘featureData’
rownames,GenoSet : .local: no visible global function definition for
  ‘featureData’
rownames<-,GenoSet: no visible global function definition for ‘fData<-’
rownames<-,GenoSet: no visible global function definition for
  ‘assayData’
rownames<-,GenoSet: no visible global function definition for
  ‘assayData<-’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘prove.R’ [25s/22s]
  Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...19,24c19,24
<     anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
<     do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
<     is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
<     pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
<     rownames, sapply, setdiff, sort, table, tapply, union, unique,
<     unlist, unsplit
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
>     as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
>     eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
>     mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
>     rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
>     unique, unlist, unsplit
32d31
< Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
39d37
< Working on segmentation for sample number 2 : a2
40a39
> Working on segmentation for sample number 2 : a2
52c51
< RUNIT TEST PROTOCOL -- Thu Oct  8 23:21:16 2015 
---
> RUNIT TEST PROTOCOL -- Tue Mar 17 12:16:04 2015 
 [25s/23s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/genoset.Rcheck/00check.log’
for details.

* installing *source* package ‘genoset’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c bounds.c -o bounds.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c rangeSummaries.c -o rangeSummaries.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c utils.c -o utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o genoset.so bounds.o init.o rangeSummaries.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: subclass "GNCList" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "GIntervalTree" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (genoset)

name	user	system	elapsed
GenoSet-class	0.176	0.006	0.182
GenoSet	0.059	0.000	0.059
RleDataFrame-class	0.382	0.010	0.393
RleDataFrame-views	0.079	0.001	0.080
baf2mbaf	0.062	0.014	0.076
boundingIndices	0.002	0.001	0.002
calcGC	0.001	0.000	0.001
chr-methods	0.031	0.016	0.048
chrIndices-methods	0.018	0.008	0.027
chrInfo-methods	0.024	0.007	0.031
chrNames-methods	0.025	0.008	0.032
chrOrder	0.002	0.000	0.002
colnames	0.015	0.008	0.023
gcCorrect	0.006	0.001	0.007
genoPlot-methods	0.080	0.013	0.101
genoPos-methods	0.035	0.009	0.044
genome-methods	0.014	0.008	0.023
genome	0.018	0.009	0.026
genomeAxis	0.051	0.009	0.061
genoset-subset	0.338	0.010	0.347
initGenoSet	0.071	0.009	0.081
isGenomeOrder-methods	0.021	0.008	0.029
locData-methods	0.017	0.009	0.025
modeCenter	0.006	0.001	0.007
pos-methods	0.028	0.018	0.046
rangeSampleMeans	0.039	0.009	0.049
readGenoSet	0.001	0.000	0.001
rownames-methods	0.019	0.010	0.028
runCBS	2.084	0.005	2.088
segPairTable-methods	0.014	0.000	0.014
segTable-methods	1.600	0.010	1.609
segs2Rle	1.600	0.009	1.608
segs2RleDataFrame	1.663	0.010	1.674
subsetAssayData	0.017	0.009	0.026
toGenomeOrder-methods	0.195	0.012	0.297